# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 13:44:15 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N-[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(1H-imidazol-5-yl)ethyl]amino}propyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](N[C@@H](CCN[C@@H](Cc1[nH]cnc1)C(O)=O)C(O)=O)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 O7J  O7J  'N-[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(1H-imidazol-5-yl)ethyl]amino}propyl]-L-glutamic acid'  ligand  49  27  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O7J
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 O7J  O10   O  OH1   0  -0.591   1.5329   2.2919   3.0939
 O7J  C13   C  CH1   0  -0.182   2.8362   1.0630  -0.6612
 O7J  C14   C  CH2   0  -0.464   3.7401   0.0014  -1.3025
 O7J  C16   C  C     0   0.556   5.4289  -1.8189  -0.8577
 O7J  C02   C  C     0   0.525  -3.9347   1.5761  -1.0814
 O7J  C04   C  CH1   0  -0.188  -3.5362   0.2281  -0.4900
 O7J  C07   C  CH2   0  -0.460  -0.3072   0.6917   1.3600
 O7J  C08   C  CH1   0  -0.218   1.0831   1.2397   1.0205
 O7J  C09   C  C     0   0.539   1.9266   1.3129   2.2895
 O7J  C15   C  CH2   0  -0.588   4.5029  -0.7986  -0.2559
 O7J  C19   C  C     0   0.550   2.3499   2.0262  -1.7358
 O7J  C22   C  CH2   0  -0.550  -4.8213  -0.4589   0.0188
 O7J  C23   C  CR5   0   0.346  -4.5661  -1.8194   0.5558
 O7J  C24   C  CR15  0  -0.274  -4.6511  -2.3320   1.8198
 O7J  C26   C  CR15  0   0.076  -4.0112  -3.9450   0.5908
 O7J  N05   N  NH1   0  -0.578  -2.5724   0.3166   0.5672
 O7J  N12   N  NH1   0  -0.589   1.7025   0.4536  -0.0131
 O7J  N25   N  N     0  -0.444  -4.3053  -3.6554   1.8312
 O7J  N27   N  NR15  0  -0.614  -4.1547  -2.8715  -0.2140
 O7J  O03   O  O     0  -0.438  -3.8821   2.6202  -0.4815
 O7J  O11   O  O     0  -0.434   2.8312   0.5602   2.5511
 O7J  O17   O  O     0  -0.443   5.5743  -2.0169  -2.0380
 O7J  O18   O  OH1   0  -0.596   6.0855  -2.4971   0.0781
 O7J  O21   O  OH1   0  -0.596   3.3288   2.8344  -2.1317
 O7J  H1    H  HOH1  0   0.482   2.0578   2.2893   3.9085
 O7J  H131  H  HCH1  0   0.251   3.4636   1.6519   0.0268
 O7J  H141  H  HCH2  0   0.255   3.1278  -0.6588  -1.9213
 O7J  H142  H  HCH2  0   0.265   4.4536   0.4913  -1.9650
 O7J  H041  H  HCH1  0   0.270  -3.1118  -0.3789  -1.2968
 O7J  H072  H  HCH2  0   0.245  -0.7247   1.2601   2.1951
 O7J  H071  H  HCH2  0   0.239  -0.2273  -0.3472   1.6935
 O7J  H081  H  HCH1  0   0.275   0.9530   2.2635   0.6538
 O7J  H151  H  HCH2  0   0.287   5.0916  -0.1278   0.3767
 O7J  H152  H  HCH2  0   0.282   3.8310  -1.3237   0.4284
 O7J  H222  H  HCH2  0   0.270  -5.2596   0.1481   0.8142
 O7J  H221  H  HCH2  0   0.276  -5.5593  -0.4995  -0.7866
 O7J  H241  H  HCR5  0   0.248  -4.9418  -1.8088   2.7182
 O7J  H261  H  HCR5  0   0.274  -3.6948  -4.9068   0.2174
 O7J  H2    H  HNH1  0   0.342  -2.9342   0.8811   1.3274
 O7J  H121  H  HNH1  0   0.362   1.9316  -0.4658   0.3397
 O7J  H271  H  HNR5  0   0.415  -3.9955  -2.8584  -1.2092
 O7J  H5    H  HOH1  0   0.482  -4.6762   2.3289  -2.6552
 O7J  H6    H  HOH1  0   0.480   6.6692  -3.1492  -0.3373
 O7J  H7    H  HOH1  0   0.482   3.0118   3.4166  -2.8378
 O7J  O20   O  O     0  -0.423   1.2355   2.0651  -2.1867
 O7J  C06   C  CH2   0  -0.244  -1.2567   0.7814   0.1750
 O7J  O01   O  OH1   0  -0.590  -4.3866   1.4650  -2.3240
 O7J  H061  H  HCH2  0   0.196  -1.2492   1.8125  -0.2072
 O7J  H062  H  HCH2  0   0.230  -0.8914   0.1513  -0.6378

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 O7J  N27  C26   aromatic  1.349  0.020  1.349
 O7J  N27  C23   aromatic  1.367  0.020  1.367
 O7J  C26  N25   aromatic  1.307  0.020  1.307
 O7J  O03  C02   double    1.205  0.020  1.205
 O7J  C22  C23   single    1.485  0.020  1.485
 O7J  C22  C04   single    1.543  0.020  1.543
 O7J  C23  C24   aromatic  1.367  0.020  1.367
 O7J  C02  O01   single    1.327  0.020  1.327
 O7J  C02  C04   single    1.525  0.020  1.525
 O7J  N25  C24   aromatic  1.368  0.020  1.368
 O7J  C04  N05   single    1.433  0.020  1.433
 O7J  N05  C06   single    1.449  0.020  1.449
 O7J  C06  C07   single    1.521  0.020  1.521
 O7J  O20  C19   double    1.203  0.020  1.203
 O7J  O17  C16   double    1.206  0.020  1.206
 O7J  C07  C08   single    1.532  0.020  1.532
 O7J  C15  C16   single    1.504  0.020  1.504
 O7J  C15  C14   single    1.522  0.020  1.522
 O7J  C16  O18   single    1.329  0.020  1.329
 O7J  N12  C08   single    1.439  0.020  1.439
 O7J  N12  C13   single    1.441  0.020  1.441
 O7J  C19  O21   single    1.330  0.020  1.330
 O7J  C19  C13   single    1.523  0.020  1.523
 O7J  C08  C09   single    1.525  0.020  1.525
 O7J  C13  C14   single    1.535  0.020  1.535
 O7J  C09  O11   double    1.206  0.020  1.206
 O7J  C09  O10   single    1.327  0.020  1.327
 O7J  O10  H1    single    0.850  0.020  0.980
 O7J  C13  H131  single    0.970  0.020  1.090
 O7J  C14  H141  single    0.970  0.020  1.090
 O7J  C14  H142  single    0.970  0.020  1.090
 O7J  C04  H041  single    0.970  0.020  1.090
 O7J  C06  H061  single    0.970  0.020  1.090
 O7J  C06  H062  single    0.970  0.020  1.090
 O7J  C07  H072  single    0.970  0.020  1.090
 O7J  C07  H071  single    0.970  0.020  1.090
 O7J  C08  H081  single    0.970  0.020  1.090
 O7J  C15  H151  single    0.970  0.020  1.090
 O7J  C15  H152  single    0.970  0.020  1.090
 O7J  C22  H222  single    0.970  0.020  1.090
 O7J  C22  H221  single    0.970  0.020  1.090
 O7J  C24  H241  single    0.930  0.020  1.080
 O7J  C26  H261  single    0.930  0.020  1.080
 O7J  N05  H2    single    0.890  0.020  1.040
 O7J  N12  H121  single    0.890  0.020  1.040
 O7J  N27  H271  single    0.860  0.020  1.020
 O7J  O01  H5    single    0.850  0.020  0.980
 O7J  O18  H6    single    0.850  0.020  0.980
 O7J  O21  H7    single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 O7J  H1    O10  C09   110.30  3.000
 O7J  H131  C13  N12   113.16  3.000
 O7J  H131  C13  C19   106.53  3.000
 O7J  N12   C13  C19   109.48  3.000
 O7J  H131  C13  C14   107.18  3.000
 O7J  C19   C13  C14   109.31  3.000
 O7J  N12   C13  C14   111.02  3.000
 O7J  H142  C14  H141  107.11  3.000
 O7J  H142  C14  C15   109.03  3.000
 O7J  H141  C14  C15   110.65  3.000
 O7J  H142  C14  C13   109.19  3.000
 O7J  H141  C14  C13   108.94  3.000
 O7J  C15   C14  C13   111.80  3.000
 O7J  O18   C16  O17   123.08  3.000
 O7J  O18   C16  C15   111.64  3.000
 O7J  O17   C16  C15   125.28  3.000
 O7J  O03   C02  O01   123.61  3.000
 O7J  O01   C02  C04   112.22  3.000
 O7J  O03   C02  C04   124.15  3.000
 O7J  H041  C04  N05   108.48  3.000
 O7J  H041  C04  C22   108.59  3.000
 O7J  N05   C04  C22   110.14  3.000
 O7J  H041  C04  C02   107.78  3.000
 O7J  N05   C04  C02   114.02  3.000
 O7J  C22   C04  C02   107.68  3.000
 O7J  H071  C07  H072  106.79  3.000
 O7J  H071  C07  C08   109.92  3.000
 O7J  H072  C07  C08   109.26  3.000
 O7J  H071  C07  C06   109.82  3.000
 O7J  H072  C07  C06   109.04  3.000
 O7J  C08   C07  C06   111.88  3.000
 O7J  H081  C08  N12   108.75  3.000
 O7J  H081  C08  C09   107.42  3.000
 O7J  N12   C08  C09   112.70  3.000
 O7J  H081  C08  C07   107.49  3.000
 O7J  C09   C08  C07   109.54  3.000
 O7J  N12   C08  C07   110.76  3.000
 O7J  O11   C09  C08   124.43  3.000
 O7J  O11   C09  O10   123.49  3.000
 O7J  C08   C09  O10   112.07  3.000
 O7J  H152  C15  H151  105.26  3.000
 O7J  H152  C15  C16   107.64  3.000
 O7J  H151  C15  C16   108.43  3.000
 O7J  H152  C15  C14   112.01  3.000
 O7J  H151  C15  C14   110.18  3.000
 O7J  C16   C15  C14   112.96  3.000
 O7J  O21   C19  O20   123.42  3.000
 O7J  O21   C19  C13   111.06  3.000
 O7J  O20   C19  C13   125.52  3.000
 O7J  H221  C22  H222  106.63  3.000
 O7J  H221  C22  C23   110.40  3.000
 O7J  H222  C22  C23   108.35  3.000
 O7J  H221  C22  C04   109.62  3.000
 O7J  H222  C22  C04   109.07  3.000
 O7J  C23   C22  C04   112.58  3.000
 O7J  N27   C23  C24   104.53  3.000
 O7J  C24   C23  C22   131.88  3.000
 O7J  N27   C23  C22   123.59  3.000
 O7J  H241  C24  N25   122.02  3.000
 O7J  H241  C24  C23   127.20  3.000
 O7J  N25   C24  C23   110.79  3.000
 O7J  H261  C26  N27   122.27  3.000
 O7J  H261  C26  N25   126.28  3.000
 O7J  N27   C26  N25   111.45  3.000
 O7J  H2    N05  C06   110.39  3.000
 O7J  H2    N05  C04   110.34  3.000
 O7J  C06   N05  C04   115.51  3.000
 O7J  H121  N12  C08   110.10  3.000
 O7J  H121  N12  C13   111.30  3.000
 O7J  C08   N12  C13   115.51  3.000
 O7J  C26   N25  C24   105.27  3.000
 O7J  H271  N27  C26   125.62  3.000
 O7J  H271  N27  C23   126.41  3.000
 O7J  C26   N27  C23   107.96  3.000
 O7J  H6    O18  C16   109.83  3.000
 O7J  H7    O21  C19   109.97  3.000
 O7J  H062  C06  H061  106.27  3.000
 O7J  H062  C06  N05   108.67  3.000
 O7J  H061  C06  N05   113.63  3.000
 O7J  H062  C06  C07   109.71  3.000
 O7J  H061  C06  C07   108.77  3.000
 O7J  N05   C06  C07   109.69  3.000
 O7J  H5    O01  C02   110.30  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 O7J  CONST_01  N25   C26  N27  C23     0.00   0.0  0
 O7J  CONST_02  C26   N25  C24  C23     0.00   0.0  0
 O7J  CONST_03  C26   N27  C23  C24     0.00   0.0  0
 O7J  CONST_04  N27   C26  N25  C24     0.00   0.0  0
 O7J  CONST_05  N27   C23  C24  N25     0.00   0.0  0
 O7J  CONST_06  C26   N27  C23  C22   180.00   0.0  0
 O7J  CONST_07  N25   C24  C23  C22   180.00   0.0  0
 O7J  CONST_08  H261  C26  N27  C23   180.00   0.0  0
 O7J  CONST_09  H271  N27  C23  C24   180.00   0.0  0
 O7J  CONST_10  H241  C24  N25  C26   180.00   0.0  0
 O7J  CONST_11  H7    O21  C19  C13   180.00   0.0  0
 O7J  CONST_12  H5    O01  C02  C04   180.00   0.0  0
 O7J  CONST_13  H1    O10  C09  C08   180.00   0.0  0
 O7J  CONST_14  H6    O18  C16  C15   180.00   0.0  0
 O7J  Var_01    N27   C23  C22  C04   -66.56  30.0  2
 O7J  Var_02    C16   C15  C14  C13  -178.25  30.0  1
 O7J  Var_03    O17   C16  C15  C14    -0.36  30.0  3
 O7J  Var_04    C07   C06  N05  C04  -174.33  30.0  3
 O7J  Var_05    N05   C06  C07  C08  -177.05  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 O7J  chir_01  C13  N12  C19  C14  positiv
 O7J  chir_02  C04  N05  C22  C02  negativ
 O7J  chir_03  C08  N12  C07  C09  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 O7J  plan-1  C22   0.020
 O7J  plan-1  C23   0.020
 O7J  plan-1  C24   0.020
 O7J  plan-1  C26   0.020
 O7J  plan-1  N25   0.020
 O7J  plan-1  N27   0.020
 O7J  plan-1  H241  0.020
 O7J  plan-1  H261  0.020
 O7J  plan-1  H271  0.020
 O7J  plan-2  C16   0.020
 O7J  plan-2  C15   0.020
 O7J  plan-2  O17   0.020
 O7J  plan-2  O18   0.020
 O7J  plan-2  H6    0.020
 O7J  plan-3  C02   0.020
 O7J  plan-3  C04   0.020
 O7J  plan-3  O03   0.020
 O7J  plan-3  H5    0.020
 O7J  plan-3  O01   0.020
 O7J  plan-4  O10   0.020
 O7J  plan-4  C08   0.020
 O7J  plan-4  C09   0.020
 O7J  plan-4  O11   0.020
 O7J  plan-4  H1    0.020
 O7J  plan-5  C13   0.020
 O7J  plan-5  C19   0.020
 O7J  plan-5  O21   0.020
 O7J  plan-5  H7    0.020
 O7J  plan-5  O20   0.020

